Also important to ask is: What was your APL *before* you inserted the protein? Was it realistic to begin with? If not, then start your problem solving there...
On 2012-08-19 06:16:48PM +0200, Albert wrote: > Dear All: > > I am using GridMAT-MD to calculate the area/lipid for my POPC system. > The whole system was consist of a 300aa protein, 116 POPC and 0.15M NaCl. > > > 1. I calculate the area/lipids by GridMAT-MD with the protein in it and > I got a value: > > Ave APL = 54.1013569676733 sq. Ang > > 2. I removed the protein and I get another value: > > Ave APL = 76.1121752016697 sq. Ang > > Do you have any idea what happen for my calculation? Of course I truned > the line "protein yes/no" for case with/without protein in the > example param file. What need to mention is that both values are far > from the POPC real area/lipids which should be something around 64. > > Does anybody knows what happen? > > thank you very much > > best > Albert > > > here is paramters: > > > ###### Input file and input file parameters > > bilayer eq-withProtein.gro > solvent SOL > ions NA+,CL- > > resname POPC > atomname P1,C1 > > ###### Define the size and shape of the grid > > box_size vectors > vectors 6.57174,6.89896,9.23361 > grid 20 > conserve_ratio yes > > ###### Define whether there is a protein embedded in the bilayer > > protein yes > precision 1.3 > P_value 5.0 > > ###### Define the desired output files > > top_pbc no > bottom_pbc no > average_pbc no > > top_area yes > bottom_area yes > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
